Another line of thought....after checking thermostats, pump, and water flow, you may want to look at the fuel system. You mentioned that performance was off on one engine. An engine that is running rich will run cooler. It should be simple to check. Is one engine smoking more than the other?

Or it may be as simple as it was for me on my T6-354 the thermostat was not sealing arond it self in the housing. Opened up and installed a small o-ring to seal properly and after that engine keeps correct temp regardles of load!

This is completely backwards. Diesels don't operate like gassers in regards to rich vs lean and the heat produced. Not calling Lollipop out, just want to let folks know when diagnosing their engine.
Also black smoke is an indication of running too rich. This can be due to too high pump tuning, washed out injector, bad or mismatched turbo, or plugged air intake. When it comes to turbos, bigger is NOT better. If not reasonably proportioned to the engine's displacement:rpm and fuel tune it won't spool properly and can result in damagingly high EGTS.

Sorry for the hi-jack, just trying to help folks understand their engine a bit more.

Back to the cooler running engine...My guess is that the thermostat has failed. Most diesel thermostats have a fail safe and when they fail it's in the open position...consequently, a cooler running engine...and just to let you know, diesel engines prefer to run a little warmer than 120 deg. Anyway, that's the first thing I'd do, swap out that thermostat.